*** What method did you use? What genesets did you use? Make sure to specify versions and cite your methods.***
GSEA analysis were carried out through the software-GSEA.4.0.3 was used and downloaded from [https://www.gsea-msigdb.org/gsea/downloads.jsp#msigdb Download.GSEA]
Geneset used are: #
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/Publication Image /GSEA-parameters.png')
Figure 1: Screen shot of the GSEA analysis parameters. The ranked gene list is ranked on its gene’s signal-to-noise ratio in descending order. 1000 permutation based on phenotype with no-collapse gene symbol were selected.
load("~/Academic/BCB420/ASS-1/Assignment 1 finals /exp.filtered.RData")
cpms.exp.filtered <- edgeR::cpm(exp.filtered[,-10])
rownames(cpms.exp.filtered) <- exp.filtered[,10]
cpms.exp.filtered <- cpms.exp.filtered[,-c(7:9)]
write.table(cpms.exp.filtered, 'cpms.exp.filtered.txt', sep = "\t", quote = F)
# Screenshot (.png) of the 'phenotype.cls' file
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/Phenotype.png')
Figure 2: Screenshot of the phenotype.cls document used in GSEA 4.0.3.
What genesets did you use?
*** Six genesets (with screenshots) were selected as shown below. *** 1. ‘h.all.v7.1.symbols.gt’ from [Hallmarks] 2. c2.cp.Biocarta.v7.1.symbols.gmt [Curated] 3. c2.cp.Kegg.v7.1.symbols.gmt [Curated] 4. c2.cp.Reactome.v7.1.symbols.gmt [Curated] 5. c2.cp.pid.v7.1.symbols.gmt [Curated] 6. ’c5.all.v7.1.symbols.gmt [GO]
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/Genesets/Hallmarks.png')
Figure 3: One geneset from Hallmark database. The gene set of ’ h.all.v7.1.symbols.gmt ’from the Hallmark database were selected for GSEA.
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/Genesets/curated4.png')
Figure 4: Four genesets - biocarta, kegg, pid and reactome - from the Curated database were selected for GSEA. More specifically, 1) c2.cp.Biocarta.v7.1.symbols.gmt [Curated] 2) c2.cp.Kegg.v7.1.symbols.gmt [Curated] 3) c2.cp.Reactome.v7.1.symbols.gmt [Curated] 4) c2.cp.pid.v7.1.symbols.gmt [Curated]
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/Genesets/GOgeneset.png')
Figure 5: One geneset was selected from Gene Ontology Database. The ‘c5.all.v7.1.symbols.gmt’ geneset from GO was selected as the last gene set for GSEA.
read.csv(file = '/Users/haoanwang./Academic/BCB420/Ass3/Nonremitters.csv')
Table 1: List of up-regulated pathways among nonremitters identified through running GSEA 4.0.3 with the ‘phenotype.cls’ and six selected genesets. The pathways are ranked based on their NES score in ascending order, with the top pathways being those with the highest absolute value of their NES score among NR samples.
read.csv(file = '/Users/haoanwang./Academic/BCB420/Ass3/Healthy.csv')
Table 1: List of down-regulated pathways among Healthy control group, identified through running GSEA 4.0.3 with ‘phenotype.cls’ and six selected genesets. Pathways are ranked based on their NES score in descending order.
6(a)
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/GSEA.result/ranked_list_corr_2.png')
6(B)
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/GSEA.result/pvalues_vs_nes_plot.png')
6(C)
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/GSEA.result/butterfly_plot.png')
Figure 6: (a) Ranked Gene List Correlation Profile shows the change in signal-to-noise ratio - Y axis-plotted against Gene position number across the gene lists. (b) The P-value (black) and FDR (red) plotted against NES. (c) Butterfly plot of NR (blue) and H (red)
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/Heat.map.1LL.001.jpeg')
Figure 7: Heat map generated from non-thresholded analysis (Healthy minus NR). Blue represent up-regulation in NR whereas red represent up-regulation in Healthy population. The y-axis is the individual gene names and the x-axis is the sample observations- three replicates from both Healthy and Nonremitters.
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/EA.H_nr.png')
Figure 8: A collection of 21 Enrichment Plot where H-enriched pathways were found. For each plot, the x-axis is the position number of genes and the y-axis is the Enrichment Score (ES). H-enriched genes all have positive ESs, sharing one characteristic pattern where ES climb up almost uninterrutedly from the start before reaching the peak and going downwards until reaching the x-axis. Each vertical black line refer to one enriched gene.
knitr::include_graphics('/Users/haoanwang./Academic/BCB420/Ass3/EA.NR_H.png')